jandot-ruby-ucsc-api 0.9

data/bin/ucsc

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+#!/usr/bin/ruby
+system("irb -r irb/completion -r rubygems -r bio -r ucsc")

data/lib/ucsc.rb

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+begin
+  require 'bio'
+  rescue nil
+end
+
+class Range
+  def contained_by?(other_range)
+    if self.begin > other_range.begin and self.end < other_range.end
+      return true
+    else
+      return false
+    end
+  end
+  
+  def overlaps_with?(other_range)
+    if ((self.begin >= other_range.begin and self.begin <= other_range.end) or (other_range.begin >= self.begin and other_range.begin <= self.end))
+      return true
+    else
+      return false
+    end
+  end
+end
+
+# Database connection
+require File.dirname(__FILE__) + '/ucsc/db_connection.rb'
+include Ucsc::Hg18
+Ucsc::Hg18::DBConnection.connect
+
+# Core modules
+require File.dirname(__FILE__) + '/ucsc/hg18/activerecord.rb'
+require File.dirname(__FILE__) + '/ucsc/hg18/slice.rb'
+
+ALL_CNPS = [Dgv, CnpIafrate, CnpLocke, CnpRedon, CnpSebat, CnpSharp, CnpTuzun]
+SEGDUPS = [GenomicSuperDup]
+ALL_REPEATS = [SimpleRepeat, ExaptedRepeat, InterruptedRepeat, Microsatellite]

data/lib/ucsc/db_connection.rb

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+require 'rubygems'
+require 'activerecord'
+
+DB_ADAPTER = 'mysql'
+DB_HOST = 'genome-mysql.cse.ucsc.edu'
+DB_USERNAME = 'genome'
+DB_PASSWORD = ''
+
+module Ucsc
+  module Hg18
+    # = DESCRIPTION
+    # The Ucsc::Hg18::DBConnection is the actual connection established
+    # with the UCSC mysql server.
+    class DBConnection < ActiveRecord::Base
+      self.abstract_class = true
+
+      # = DESCRIPTION
+      # The Ucsc::Hg18::DBConnection#connect method makes the connection
+      # to the UCSC hg18 database.
+      #
+      # = USAGE
+      #  # Connect to the hg18
+      #  Ensembl::Core::DBConnection.connect
+      #
+      # ---
+      # *Arguments*: none
+      def self.connect
+        establish_connection(
+                            :adapter => DB_ADAPTER,
+                            :host => DB_HOST,
+                            :database => 'hg18',
+                            :username => DB_USERNAME,
+                            :password => DB_PASSWORD
+                            )
+        end
+
+      end
+
+    end
+
+  end

data/lib/ucsc/hg18/activerecord.rb

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+#
+# = ucsc/hg18/activerecord.rb - ActiveRecord mappings to UCSC hg18 database
+#
+# Copyright::   Copyright (C) 2008 Jan Aerts <jan.aerts@gmail.com>
+# License::     The Ruby License
+#
+
+# = DESCRIPTION
+# == What is it?
+# The UCSC module provides an API to the UCSC databases
+# stored at genome-mysql.cse.ucsc.edu. This is the same information that is
+# available from http://genome.ucsc.edu
+#
+# The Ucsc::Hg18 module covers the hg18 (= NCBI build 36) assembly.
+#
+# == ActiveRecord
+# The UCSC API provides a ruby interface to the UCSC mysql databases
+# at genome-mysql.cse.ucsc.edu. Most of the API is based on ActiveRecord to
+# get data from that database. In general, each table is described by a
+# class with the same name: the cnpRedon table is covered by the
+# CnpRedon class, the dgv table is covered by the Dgv class,
+# etc. As a result, accessors are available for all columns in each table.
+# For example, the cnpRedon table has the following columns: chrom, chromStart, 
+# chromEnd and name. Through ActiveRecord, these column names become available 
+# as attributes of CnpRedon objects:
+#   puts my_cnp_redon.name
+#   puts my_cnp_redon.chrom
+#   puts my_cnp_redon.chromStart
+#   puts my_cnp_redon.chromEnd
+#
+# ActiveRecord makes it easy to extract data from those tables using the
+# collection of #find methods. There are three types of #find methods (e.g.
+# for the CnpRedon class):
+# a. find based on primary key in table:
+#  # not possible with the UCSC database
+# b. find_by_sql:
+#  my_cnp = CnpRedon.find_by_sql('SELECT * FROM cnpRedon WHERE name = 'cnp1'")
+# c. find_by_<insert_your_column_name_here>
+#  my_cnp = CnpRedon.find_by_name('cnp1')
+#  my_cnp2 = CnpRedon.find_by_chrom_and_chromStart('chr1',377)
+# To find out which find_by_<column> methods are available, you can list the
+# column names using the column_names class methods:
+#
+#  puts Ucsc::Hg18::CnpRedon.column_names.join("\t")
+#
+# For more information on the find methods, see
+# http://ar.rubyonrails.org/classes/ActiveRecord/Base.html#M000344
+#
+module Ucsc
+  # = DESCRIPTION
+  # The Ucsc::Hg18 module covers the hg18 database from
+  # genome-mysql.cse.ucsc.edu and covers mainly sequences and their annotations.
+  # For a more information about the database tables, click on the "Describe 
+  # table schema" in the Table Browser.
+  module Hg18
+    # = DESCRIPTION
+    # The Sliceable mixin holds the get_slice method and can be included
+    # in any class that lends itself to having a position on a chromosome.
+    module Sliceable
+      def slice
+        start, stop, strand = nil, nil, nil
+      	if self.class.column_names.include?('chromStart')
+          start = self.chromStart
+        end
+      	if self.class.column_names.include?('chromEnd')
+          stop = self.chromEnd
+        end
+      	if self.class.column_names.include?('strand')
+          strand = self.strand
+        end
+      
+        return Ucsc::Hg18::Slice.new(self.chrom, Range.new(start.to_i, stop.to_i), strand)
+      end
+    end
+    
+    # = DESCRIPTION
+    # The Feature mixin holds common methods for all feature-like classes, such 
+    # as how to print itself to the screen.
+    module Feature
+      include Sliceable
+      
+      def to_s
+        return self.class.to_s + "\t" + self.slice.to_s + "\t" + self.name
+      end
+    end
+    
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "All hybridizations were performed in duplicate incorporating a 
+    # dye-reversal using proprietary 1 Mb GenomeChip V1.2 Human BAC Arrays 
+    # consisting of 2,632 BAC clones (Spectral Genomics, Houston, TX). The 
+    # false positive rate was estimated at ~1 clone per 5,264 tested."
+    class CnpIafrate < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'cnpIafrate2'
+      set_primary_key nil
+    end
+
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "DNA samples were obtained from Coriell Cell Repositories. The reference 
+    # DNA used for all hybridizations was from a single male of Czechoslovakian 
+    # descent, Coriell ID GM15724 (also used in the Sharp study).
+    # 
+    # A locus was considered a CNV (copy number variation) if the log ratio of 
+    # fluroescence measurements for the individuals assayed exceeded twice the 
+    # standard deviation of the autosomal clones in replicate dye-swapped 
+    # experiments. A CNV was classified as a CNP if altered copy number was 
+    # observed in more than 1% of the 269 individuals."
+    class CnpLocke < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'cnpLocke'
+      set_primary_key nil
+    end
+
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "Experiments were performed with the International HapMap DNA and 
+    # cell-line collection using two technologies: comparative analysis of 
+    # hybridization intensities on Affymetric GeneChip Human Mapping 500K early 
+    # access arrays (500K EA) and comparative genomic hybridization with a 
+    # Whole Genome TilePath (WGTP) array."
+    class CnpRedon < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'cnpRedon'
+      set_primary_key nil
+    end
+
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "Following digestion with BglII or HindIII, genomic DNA was hybridized to 
+    # a custom array consisting of 85,000 oligonucleotide probes. The probes 
+    # were selected to be free of common repeats and have unique homology 
+    # within the human genome. The average resolution of the array was ~35kb; 
+    # however, only intervals in which three consecutive probes showed 
+    # concordant signals were scored as CNPs. All hybridizations were performed 
+    # in duplicate incorporating a dye-reversal, with the false positive rate 
+    # estimated to be ~6%."
+    class CnpSebat < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'cnpSebat2'
+      set_primary_key nil
+    end
+
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "All hybridizations were performed in duplicate incorporating a 
+    # dye-reversal using a custom array consisting of 2,194 end-sequence or 
+    # FISH-confirmed BACs, targeted to regions of the genome flanked by 
+    # segmental duplications. The false positive rate was estimated at ~3 
+    # clones per 4,000 tested."
+    class CnpSharp < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'cnpSharp2'
+      set_primary_key nil
+    end
+
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "Paired-end sequences from a human fosmid DNA library were mapped to the 
+    # assembly. The average resolution of this technique was ~8kb, and included 
+    # 56 sites of inversion not detectable by the array-based approaches. 
+    # However, because of the physical constraints of fosmid insert size, this 
+    # technique was unable to detect insertions greater than 40 kb in size."
+    class CnpTuzun < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'cnpTuzun'
+      set_primary_key nil
+    end
+    
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # ""
+    class Dgv < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'dgv'
+      set_primary_key nil
+      
+      def to_s
+        return self.class.to_s + "\t" + self.slice.to_s + "\t" + self.reference + "\t" + self.method
+      end
+    end
+    
+    
+    # = DESCRIPTION
+    # From Simple Repeats description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "This track displays simple tandem repeats (possibly imperfect) located 
+    # by Tandem Repeats Finder (TRF), which is specialized for this purpose. 
+    # These repeats can occur within coding regions of genes and may be quite 
+    # polymorphic. Repeat expansions are sometimes associated with specific 
+    # diseases."
+    class SimpleRepeat < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'simpleRepeat'
+      set_primary_key nil
+    end
+    
+    # = DESCRIPTION
+    # From Structural Variants description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "This track shows regions detected as putative genomic duplications 
+    # within the golden path. The following display conventions are used to 
+    # distinguish levels of similarity:
+    #   * Light to dark gray: 90 - 98% similarity
+    #   * Light to dark yellow: 98 - 99% similarity
+    #   * Light to dark orange: greater than 99% similarity
+    #   * Red: duplications of greater than 98% similarity that lack sufficient 
+    #   Segmental Duplication Database evidence (most likely missed overlaps) 
+    # For a region to be included in the track, at least 1 Kb of the total 
+    # sequence (containing at least 500 bp of non-RepeatMasked sequence) had 
+    # to align and a sequence identity of at least 90% was required."
+    class GenomicSuperDup < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'genomicSuperDups'
+      set_primary_key nil
+    end
+    
+    # = DESCRIPTION
+    # From Exapted Repeat description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "This track displays conserved non-exonic elements that have been 
+    # deposited by mobile elements (repeats), a process termed "exaptation" 
+    # (Gould et al., 1982). These regions were identified during a genome-wide 
+    # survey (Lowe et al., 2007) with the expectation that regions of this type 
+    # may act as distal transcriptional regulators for nearby genes. A previous 
+    # case study experimentally verified an exapted mobile element acting as a 
+    # distal enhancer (Bejerano et al. , 2006)."
+    class ExaptedRepeat < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'exaptedRepeats'
+      set_primary_key nil
+    end
+
+#TODO: The repeatmasker features are distributed over different tables; one for
+#      each chromosome.
+#    # = DESCRIPTION
+#    # From RepeatMasker description page when clicking the "Describe 
+#    # table schema" in the table browser:
+#    # "This track was created by using Arian Smit's RepeatMasker program, which 
+#    # screens DNA sequences for interspersed repeats and low complexity DNA 
+#    # sequences. The program outputs a detailed annotation of the repeats that 
+#    # are present in the query sequence, as well as a modified version of the 
+#    # query sequence in which all the annotated repeats have been masked. 
+#    # RepeatMasker uses the RepBase library of repeats from the Genetic 
+#    # Information Research Institute (GIRI). RepBase is described in Jurka, J. 
+#    # (2000) in the References section below."
+#    class RepeatMasker < DBConnection
+#      include Ucsc::Hg18::Feature
+#      
+#      set_table_name 'rmsk'
+#      set_primary_key nil
+#    end
+
+    # = DESCRIPTION
+    # From Interrupted Repeat description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "This track shows joined fragments of interrupted repeats extracted from 
+    # the output of the RepeatMasker program, which screens DNA sequences for 
+    # interspersed repeats and low complexity DNA sequences using the RepBase 
+    # library of repeats from the Genetic Information Research Institute (GIRI). 
+    # RepBase is described in Jurka, J. (2000) in the References section below.
+    #
+    # The detailed annotations from RepeatMasker are in the RepeatMasker track. 
+    # This track shows fragments of original repeat insertions which have been 
+    # interrupted by insertions of younger repeats or through local 
+    # rearrangements. The fragments are joined using the ID column of 
+    # RepeatMasker output."
+    class InterruptedRepeat < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'nestedRepeats'
+      set_primary_key nil
+    end
+    
+    # = DESCRIPTION
+    # From Microsatellite description page when clicking the "Describe 
+    # table schema" in the table browser:
+    # "This track displays regions that are likely to be useful as 
+    # microsatellite markers. These are sequences of at least 15 perfect 
+    # di-nucleotide and tri-nucleotide repeats, and tend to be highly 
+    # polymorphic in the population."
+    class Microsatellite < DBConnection
+      include Ucsc::Hg18::Feature
+      
+      set_table_name 'microsat'
+      set_primary_key nil
+    end
+
+  end
+end

data/lib/ucsc/hg18/slice.rb

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+module Ucsc
+  module Hg18
+    class Slice
+      def initialize(chromosome, range, strand = nil)
+        @chromosome, @range = chromosome, range, strand
+      end
+      attr_accessor :chromosome, :range, :strand
+      
+      def to_s
+        return @chromosome + ':' + @range.to_s
+      end
+      
+      def overlaps?(other_slice)
+        if self.chromosome != other_slice.chromosome
+          return false
+        end
+        
+        if self.range.overlaps?(other_slice.range)
+          return true
+        else
+          return false
+        end
+      end
+      
+      def contained_by?(other_slice)
+        if self.chromosome != other_slice.chromosome
+          return false
+        end
+        
+        if self.range.contained_by?(other_slice.range)
+          return true
+        else
+          return false
+        end
+      end
+      
+      def contains?(other_slice)
+        if self.chromosome != other_slice.chromosome
+          return false
+        end
+        
+        if self.range.contains?(other_slice.range)
+          return true
+        else
+          return false
+        end
+      end
+    end
+  end
+end

data/samples/ranges.txt

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+chrX	365739	366104
+chrX	435678	436376
+chrX	823067	823982
+chrX	827850	828111
+chrX	830087	830927
+chrX	839913	840259
+chrX	1386851	1388015
+chrX	1574525	1574825
+chrX	1852006	1852321
+chrX	1871048	1871715
+chr5	1881979	1882347
+chr5	1997045	1997838
+chr5	2204818	2205098
+chr5	3044350	3044625
+chr5	3473977	3475116
+chr3	4100974	4103932
+chr3	4536840	4537115
+chr3	4914689	4915030

data/samples/tryout.rb

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+#!/usr/bin/ruby
+require 'yaml'
+require '../lib/ucsc.rb'
+
+ranges = Hash.new
+File.open('ranges.txt').each do |line|
+  line.chomp!
+  chromosome, start, stop = line.split(/\t/)
+  target_slice = Slice.new(chromosome, Range.new(start.to_i, stop.to_i))
+  if ! ranges.keys.include?(chromosome)
+    ranges[chromosome] = Array.new
+  end
+  ranges[chromosome].push(target_slice)
+end
+
+ranges.keys.each do |chromosome|
+  all_annotations = Array.new
+
+  ALL_CNPS.each do |klass|
+    all_annotations.push(klass.find_all_by_chrom(chromosome))
+  end
+
+  ALL_REPEATS.each do |klass|
+    all_annotations.push(klass.find_all_by_chrom(chromosome))
+  end
+  
+  all_annotations.flatten!
+
+  ranges[chromosome].each do |target_slice|
+    all_annotations.each do |annotation|
+      if annotation.slice.overlaps?(target_slice)
+        puts target_slice.to_s + "\t" + annotation.to_s
+      end
+    end
+  end
+end

data/test/unit/test_activerecord.rb

@@ -0,0 +1,94 @@
+#
+# = test/unit/test_activerecord.rb - Unit test for Ucsc::Hg18
+#
+# Copyright::   Copyright (C) 2008
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+
+require 'ucsc'
+
+include Ucsc::Hg18
+
+# Let's see if we can 'find' things
+class SimpleRecordsTest < Test::Unit::TestCase
+  def test_iafrage
+    assert_equal('CTC-232B23', CnpIafrate.find_by_name('CTC-232B23').name)
+  end
+
+  def test_locke
+    assert_equal('RP11-430E19', CnpLocke.find_by_name('RP11-430E19').name)
+  end
+
+  def test_redon
+    assert_equal('cnp1', CnpRedon.find_by_name('cnp1').name)
+  end
+
+  def test_sebat
+    assert_equal(1, CnpSebat.find_all_by_chrom_and_chromStart('chr1',12826893).length)
+  end
+
+  def test_sharp
+    assert_equal('RP11-430E19', CnpSharp.find_by_name('RP11-430E19').name)
+  end
+
+  def test_tuzun
+    assert_equal('chr1.1', CnpTuzun.find_by_name('chr1.1').name)
+  end
+
+  def test_dgv
+    assert_equal('31596', Dgv.find_by_name('31596').name)
+  end
+
+  def test_simple_repeats
+    assert_equal('TAACCC', SimpleRepeat.find_by_chrom_and_chromStart('chr1', 0).sequence)
+  end
+  
+  def test_genomic_super_dup
+    assert_equal('chr2:114046768', GenomicSuperDup.find_by_chrom_and_chromStart('chr1',465).name)
+  end
+  
+  def test_exapted_repeat
+    assert_equal(3180908, ExaptedRepeat.find_by_name('exap1').chromStart)
+  end
+  
+#  def test_repeatmasker
+#    
+#  end
+  
+  def test_interrupted_repeat
+    assert_equal('L2', InterruptedRepeat.find_by_chrom_and_chromStart('chr1',13687).name)
+  end
+  
+  def test_microsatellite
+    assert_equal('16xGT', Microsatellite.find_by_chrom_and_chromStart('chr1', 40344).name)
+  end
+end
+
+class MixinsTest < Test::Unit::TestCase
+  def test_feature
+    assert_equal(true, CnpIafrate.include?(Feature))
+    assert_equal(true, CnpLocke.include?(Feature))
+    assert_equal(true, CnpRedon.include?(Feature))
+    assert_equal(true, CnpSebat.include?(Feature))
+    assert_equal(true, CnpSharp.include?(Feature))
+    assert_equal(true, CnpTuzun.include?(Feature))
+    assert_equal(true, Dgv.include?(Feature))
+  end
+  
+  def test_sliceable
+    assert_equal(true, CnpIafrate.include?(Sliceable))
+    assert_equal(true, CnpLocke.include?(Sliceable))
+    assert_equal(true, CnpRedon.include?(Sliceable))
+    assert_equal(true, CnpSebat.include?(Sliceable))
+    assert_equal(true, CnpSharp.include?(Sliceable))
+    assert_equal(true, CnpTuzun.include?(Sliceable))
+    assert_equal(true, Dgv.include?(Sliceable))
+  end
+end

metadata

@@ -0,0 +1,77 @@
+--- !ruby/object:Gem::Specification 
+name: jandot-ruby-ucsc-api
+version: !ruby/object:Gem::Version 
+  version: "0.9"
+platform: ruby
+authors: 
+- Jan Aerts
+autorequire: ucsc
+bindir: bin
+cert_chain: []
+
+date: 2008-08-13 00:00:00 -07:00
+default_executable: ucsc
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: bio
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "1"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: activerecord
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+description: ruby-ucsc-api provides a ruby API to the UCSC databases (http://genome.ucsc.edu)
+email: jan.aerts@gmail.com
+executables: 
+- ucsc
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- bin/ucsc
+- lib/ucsc/db_connection.rb
+- lib/ucsc/hg18/activerecord.rb
+- lib/ucsc/hg18/slice.rb
+- lib/ucsc.rb
+- samples/ranges.txt
+- samples/tryout.rb
+- test/unit/test_activerecord.rb
+has_rdoc: true
+homepage: http://github.com/jandot/ruby-ucsc-api
+post_install_message: 
+rdoc_options: 
+- --exclude .
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 2
+summary: API to UCSC databases
+test_files: 
+- test/unit/test_activerecord.rb